Is there a way to bake animated/ deformed geometry?
You can export most animations as point cache files (*.pc2) and read them back in using the Mesh Cache modifier. The export addon is not active as default so you have to enable it beforehand.



To read it back in, use the Mesh Cache modifier. The option to read PC2 files is under the format option.



The PC2 format works well with 3dsMax's Point Cache modifier as well, so you can use it to transfer animations between the two programs. Not sure about Maya.

One thing you should keep in mind is that PC2 cannot save fluid simulations. Point caches require that the number of vertices remain the same between objects, and this is not the case with fluids. However it seems that a modifier for reading OBJ sequences is in the works, but that's still coming.